Recreational waters are monitored worldwide to protect bathers from infectious diseases caused by waterborne pathogens associated with the pollution of natural recreational waters by human and animal feces. Water quality standards are typically based on measurements of the concentrations of fecal indicator organisms (Escherichia coli and Enterococcus) and are becoming more stringent.

A complicating factor is the time required (18-36 hours) for completion of conventional culture-based methods (as approved by the US EPA or ISO institutions). During the lag time between sample collection and availability of results indicator and pathogen levels, weather and water conditions may change and thus related health risk may also change. By using new rapid analytical tools, critical control points can be monitored to provide information so that management actions can have an impact on the exposure risk.

The aim of this study was to evaluate the capacity of two new alternative methods for the rapid and routine enumeration of E. coli and Enterococci in bathing waters: fluorimetric assays based on the measurement of enzymatic activities, and quantitative RT-PCR. Both methods are fast (1 hour for 6 samples analysed by one fluorescence spectrophotometer; 3 hours for the simultaneous analysis of 15 to 96 samples by RT-PCR) and their results (for the microbiological criteria of current European regulations) compared with those from the standard methods are congruent in more than 81% of analysed samples. Because these methods provide a faster assessment of water quality, they have the potential to significantly reduce health risk resulting from exposure to recreational waters and also reduce errors in beach closing.